Biology subjects

Hallin, S.

Publications and source records attributed to Hallin, S..

5 recordsLinked to original sources

bioRxiv2023

Predicting genomic traits in ammonia-oxidizing archaea using phylogenetic signals

Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping, an approach not previously used for microorganisms, to predict key traits of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 168 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. Of the selected genes, 94% displayed a significant phylogenetic signal and gene presence was predicted with >88% accuracy, >88% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of traits. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and show key ecological predictions, e.g., that AOA communities in nitrogen rich soils have capacity for ureolytic metabolism while those adapted to low pH soils have the high affinity ammonia transporter (amt2). Predicting genomic traits can shed light on the potential functions that microbes perform across earth biomes, further contributing to a better mechanistic understanding of their community assembly.

ecology↗

bioRxiv2023

Spatial and temporal changes in microbial communities and greenhouse gas emissions in a denitrifying woodchip bioreactor at low water temperatures

Nitrogen (N) pollution is a major threat to ecosystems and a driver of climate change through emissions of the greenhouse gas nitrous oxide (N2O). Mining activities are increasingly recognized for contributing to N pollution due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities in pore water and woodchips and their genetic potential for different N transformation processes, and how this affected the N removal capacity and possible production of undesired N species, like ammonium, nitrite and N2O. About 80 and 65 % of the nitrate was removed from the leachate the first and second operational year, respectively, which agreed with a decrease in dissolved organic carbon in the outlet water. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in the genetic potential for N cycling and ultimately also reactor performance. We conclude that DNRA had minimal impact on the overall N removal efficiency due to the low relative abundance of the key gene nrfA involved in DNRA and the low production of ammonium. However, nitrite, ammonium, and N2O were formed in the bioreactor and released in the effluent water, although direct emissions of N2O from the surface was low. The N2O production in the reactor might be explained by the ratio between the genetic potential for overall denitrification and N2O reduction in the woodchip and pore water communities, as indicated by the low ratio between the abundance of nir and nosZ genes. Altogether, the results indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length, and that unwanted reactive N species were produced at different time points and locations in the reactor. Thus, the succession of microbial communities in woodchip denitrifying bioreactors treating mining impacted water develops slowly at low temperature, which impacts the reactor performance.

ecology↗

bioRxiv2023

Phyloecology of nrfA-ammonifiers and their relative importance with denitrifiers in global terrestrial biomes

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of nitrate ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screened more than 1 million genomes for nrfA, encoding the nitrite reductase in nitrate ammonification. Nearly 50% of the nitrate ammonifier assemblies carry at least one denitrification gene and, contrary to the current paradigm, have higher potential for nitrous oxide production than reduction. We then used a phylogeny-based approach to recruit nrfA and denitrification nitrite reductase gene fragments in 1,861 metagenomes covering the major terrestrial biomes. Denitrification genes dominated, except in tundra, and random forest modelling teased apart the influence of the soil C/N on nitrate ammonifier vs denitrifier abundances, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and the factors ultimately controlling the fate of nitrate in soil.

microbiology↗

bioRxiv2022

Distribution and environmental drivers of fungal denitrifiers in global soils

The microbial process denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase and are potential sources of N2O. Still, their diversity, distribution, and environmental determinants in terrestrial ecosystems remain unresolved. We used a phylogenetically informed approach to screen 1 980 soil and rhizosphere metagenomes representing 608 globally distributed sampling sites for the denitrification marker gene nirK, coding for nitrite reductase. We show that fungal denitrifiers are sparse, yet cosmopolitan and dominated by saprotrophs and opportunistic plant pathogens. Few showed biome-specific distribution patterns. However, members of the Fusarium oxysporum species complex, known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands but were most abundant in forest soils. The overall low abundance of fungal relative to bacterial and archaeal denitrifiers suggests that their role in denitrification and contribution to soil N2O emissions may be less important than previously suggested. Nevertheless, in relative terms, they could play a role in soils characterized by high carbon to nitrogen ratio and low pH, especially in tundra and boreal and temperate coniferous forests. Our results further indicate that plant-pathogen interactions may favor fungal denitrifiers. Thus, increasing global warming with predicted proliferation of pathogens and the fact that many of the fungi with nirK detected in the metagenomes are stress-tolerant cosmopolitans suggest that fungal denitrifier abundance may increase in terrestrial ecosystems.

microbiology↗

bioRxiv2022

Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics

Microorganisms are key players in the global cycling of nitrogen (N) and carbon (C), controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide (N2O) and methane (CH4). Characterizing the microbial functional guilds driving these processes is crucial for understanding ecosystem functioning and predicting their responses to environmental changes. Standard sequence-based characterization methods often reveal only a limited fraction of their diversity in nature because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of PCR-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic N and CH4 cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264,000 unique probes. These probes were used to selectively enrich the target genes in shotgun metagenomic libraries. In validation experiments with the mock communities of known microorganisms, targeted metagenomics yielded gene profiles similar to those of the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics from agricultural and wetland soils were significantly correlated, indicating that the targeted approach did not introduce significant quantitative bias. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Notably, shotgun metagenomics detected only three out of the 84 amoA gene phylotypes detected using targeted metagenomics. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes. Manuscript contribution to the fieldMetagenomic sequencing often yields limited numbers of sequences of rare microbial taxa or functional genes, preventing in-depth analyses of specific populations and functional groups. Amplicon-based approaches enable the higher diversity coverage of target populations, but the drawback is the difficulty in designing unbiased primers that cover the highest intra-group diversity. Targeted metagenomics overcomes these challenges and results in similar community structure as traditional amplicon sequencing, while expanding the sequence space in a less biased metagenomic-based approach. Therefore, targeted metagenomics is an invaluable tool for studying the diversity of specific populations within complex natural microbiomes. Here, we present and evaluate a probe library designed for targeted metagenomics of nitrogen and methane cycling genes in complex communities.

microbiology↗